BN1849 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 5 8.0931e-06 5.4703e-04
Layer 3 1.0360e-05 2.4821e-02
Layer 4 1.6968e-05 1.9601e-03
Layer 6 5.8213e-05 9.5804e-04
Layer 2 7.9357e-05 1.9747e-02
WM 9.5619e-01 4.7331e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 6 2.4453 0.7851
FKBP8 Layer 5 2.3867 0.7594
GOT1 Layer 5 2.3711 0.7585
STMN3 Layer 5 2.2871 0.7542
RTL8C Layer 6 2.2461 0.7532
MGST3 Layer 5 2.3496 0.7526
ATP6V1G2 Layer 5 2.4238 0.7522
SNU13 Layer 5 2.1973 0.7496
SYN1 Layer 6 2.2324 0.7490
PINK1 Layer 5 2.3496 0.7469
PI4KA Layer 6 2.2520 0.7462
ARHGDIG Layer 6 2.4941 0.7447
GRIN1 Layer 4 2.2461 0.7445
PRDX2 Layer 5 2.3213 0.7440
CEND1 Layer 5 2.3926 0.7440
SELENOH Layer 5 2.2617 0.7438
NAPA Layer 6 2.2363 0.7437
ARL6IP1 Layer 5 2.2227 0.7420
CABP1 Layer 4 2.3184 0.7409
PTPRN Layer 6 2.2363 0.7394
RAN Layer 6 2.2930 0.7392
LRPAP1 Layer 5 2.2773 0.7388
ATP6V0D1 Layer 6 2.4180 0.7380
SYT4 Layer 6 2.3340 0.7377
WBP2 Layer 5 2.2715 0.7373
TOLLIP Layer 4 2.3281 0.7373
KLC1 Layer 6 2.3086 0.7370
NDRG4 Layer 4 2.2168 0.7369
IQSEC1 Layer 5 2.2617 0.7358
EEF1A2 Layer 5 2.3242 0.7355
SYP Layer 5 2.3926 0.7351
ATP5MC3 Layer 5 2.2871 0.7347
BMERB1 Layer 5 2.2969 0.7344
SEZ6L2 Layer 6 2.2930 0.7335
RGS4 Layer 5 2.4023 0.7333
ATP5MF Layer 5 2.3125 0.7331
TCEAL7 Layer 5 2.2461 0.7330
GPI Layer 6 2.2363 0.7324
ACOT7 Layer 6 2.3555 0.7323
SNAP91 Layer 5 2.3184 0.7322
UBA1 Layer 5 2.2520 0.7311
LDHA Layer 5 2.4121 0.7311
ATP6V0E2 Layer 5 2.4238 0.7309
CPLX1 Layer 5 2.6836 0.7304
NDFIP1 Layer 5 2.1973 0.7290
TUBB3 Layer 5 2.2969 0.7288
SLC25A3 Layer 5 2.2773 0.7288
SULT4A1 Layer 5 2.3623 0.7286
PHYHIP Layer 6 2.2832 0.7286
FAIM2 Layer 5 2.2773 0.7282

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1849
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1849_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1849/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1849/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1849/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1849/report/PD/BN1849_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1849/report/PD/BN1849_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 08:44:52
  • Number of Processes: 10
  • Spending Time: 0h 4m